Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq

Authors: WU, QIBIN - Fujian Agriculture And Forest University; SU, YACHUN - Fujian Agriculture And Forest University; Pan, Yong-Bao; XU, FU - Fujian Agriculture And Forest University; ZOU, WENHUI - Fujian Agriculture And Forest University; QUE, BEIBEI - Fujian Agriculture And Forest University; LIN, PEIXIA - Fujian Agriculture And Forest University; SUN, TINGTING - Fujian Agriculture And Forest University; GRISHAM, MICHAEL - Retired ARS Employee; XU, LIPING - Yunnan Academy Of Agriculture Sciences; QUE, YOUXIONG - Fujian Agriculture And Forest University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/27/2022
Publication Date: 10/13/2022
Citation: Wu, Q., Su, Y., Pan, Y.-B., Xu, F., Zou, W., Que, B., Lin, P., Sun, T., Grisham, M.P., Xu, L., Que, Y. 2022. Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq. Frontiers in Plant Science. 13:1035266. https://doi.org/10.3389/fpls.2022.1035266.
DOI: https://doi.org/10.3389/fpls.2022.1035266

Interpretive Summary: Sugarcane smut s one of the most severe fungal diseases worldwide. Growing smut-resistant varieties is a reliable and practicable way to manage this disease. However, it takes about 12 years to breed a resistant cultivar by traditional method due to the complex genetic background of sugarcane and the polygenic nature of smut resistance. Marker-assisted selection helps reduce the number of years and costs of breeding. The objective of this study is to discover DNA markers and candidate genes that associate with smut resistance in sugarcane. A cross was made between a smut-resistant variety YT93-159 and a smut-susceptible variety ROC22 and 312 progenies were inoculated with the smut pathogen before planting into triplicated field plots at two locations. During the growing season, smut disease data were collected and used to construct two bulks of progenies. One bulk consisted of 27 highly resistant progenies and the other 24 highly susceptible progenies. Total RNA were extracted from the progenies, which were pooled to form the bulks and subject to Bulked Segregant RNA-Sequence Analysis. A total of 164.44 Gigabytes sequence data were obtained containing 2,341,449 SNPs and 64,999 candidate genes. Using a sugarcane reference genome and five different software programs, namely, STAR, GO, KEGG, 'SNP-index, and Euclidean distance, the sequence data were further analyzed to discover the following: 1). 7,295 differentially expressed genes (DEGs) between two bulks, involving in several stress-related metabolic pathways and plant-pathogen interactions; and 2). 45,946 high-quality SNPs and a 1.27 Megabytes chromosome region and 129 candidate genes that associated with smut resistance. Finally, 20 out of 24 stress-resistance associated genes were verified with the RT-qPCR laboratory method. These potential SNP markers and candidate genes are good resources for smut resistance breeding in sugarcane with important theoretical and practical application values. Based on the findings from this study and an earlier WGCNA study, a potential molecular mechanism of sugarcane and smut pathogen interaction is depicted.

Technical Abstract: Sugarcane smut caused by Sporisorium scitamineum is one of the most severe fungal diseases worldwide. Growing smut-resistant varieties is a reliable and practicable way to manage this disease. However, it takes about 12 years to breed a resistant cultivar by traditional method due to the complex genetic background of sugarcane and the polygenic nature of smut resistance. Marker-assisted selection helps reduce the number of years and costs of breeding in sugarcane. In this study, a cross was made between a smut-resistant variety YT93-159 and a smut-susceptible variety ROC22, and 312 progenies were inoculated with the smut pathogen before planting in triplicated field plots at two locations. During the growing season, smut disease data were collected and used to construct two bulks of progenies. One bulk consisted of 27 highly resistant progenies and the other 24 highly susceptible progenies. Total RNAs were extracted from the progenies of each bulk, which were pooled and subject to bulked segregant RNA-sequence analysis (BSR-Seq). A total of 164.44 Gb clean data containing 2,341,449 SNPs and 64,999 genes were obtained, 7,295 of which were differentially expressed genes (DEGs). GO and KEGG enrichment analyses showed that these DEGs were mainly enriched in stress-related metabolic pathways, including carbon metabolism, phenylalanine metabolism, plant hormone signal transduction, glutathione metabolism, and plant-pathogen interactions, etc. Using both 'SNP-index and Euclidean distance (ED) methods, 45,946 high-quality, credible SNPs, a 1.27 Mb region at S. spontaneum chromosome Chr5B (68,904,827 to 70,172,982), and 129 candidate genes were identified to be associated with smut resistance. Twenty-four genes, either encoding key enzymes involved in signaling pathways or being transcription factors, were found to be very closely associated with stress resistance. Twenty genes were amplifiable with RT-qPCR upon S. scitamineum infection and might play a positive role in smut resistance. In addition, a potential molecular mechanism of sugarcane and S. scitamineum interaction is depicted based on the results from this and an earlier WGCNA study (IJMS-1872157, in review) that activations of MAPK cascade signaling, ROS signaling, Ca2+ signaling, and PAL metabolic pathway and initiation of the glyoxalase system jointly promote the resistance to S. scitamineum in sugarcane. This study provides potential SNP markers and candidate gene resources for smut resistance breeding in sugarcane and has relatively important theoretical and practical implications.